Alignments for a candidate for thrC in Thauera aminoaromatica S2

GapMind for Amino acid biosynthesis

Alignments for a candidate for thrC in Thauera aminoaromatica S2

Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_004304059.1 C665_RS07145 threonine synthase

Query= BRENDA::Q2SWH9
         (483 letters)



>NCBI__GCF_000310185.1:WP_004304059.1
          Length = 487

 Score =  667 bits (1721), Expect = 0.0
 Identities = 342/487 (70%), Positives = 391/487 (80%), Gaps = 6/487 (1%)

Query: 1   MNYISTRG-AGIGERHTFSDILLGGLAKDGGLYLPSEYPQVSADELARWRTLPYADLAFE 59
           M Y+STRG AG      F DILLGGLA DGGLYLP  YPQV+  EL  WR L YA+LAF 
Sbjct: 1   MKYLSTRGHAGQPANPEFCDILLGGLAPDGGLYLPETYPQVTRAELDAWRGLSYAELAFA 60

Query: 60  ILSKFCDDIAAADLRAITRRTYTADVYRHARRGGNAADITPLTTL--GTENGAPVSLLEL 117
           ILSKF  DI A DL+AI  +TYTA+VYRH R GG+A DITP+  L    +    + LLEL
Sbjct: 61  ILSKFITDIPAVDLKAICAKTYTAEVYRHVRAGGDARDITPVHWLEKDADGRGRLGLLEL 120

Query: 118 SNGPTLAFKDMAMQLLGNLFEYTLAKHGETLNILGATSGDTGSAAEYAMRGKEGVRVFML 177
           SNGPTLAFKDMAMQLLGNLFEY LAK GET+NILGATSGDTGSAAEYAMRGK GVRVFML
Sbjct: 121 SNGPTLAFKDMAMQLLGNLFEYVLAKRGETINILGATSGDTGSAAEYAMRGKHGVRVFML 180

Query: 178 SPHKKMSAFQTAQMYSLQDPNIFNLAVNGVFDDCQDIVKAVSNDHAFKAQQKIGTVNSIN 237
           SPH KMSAFQ AQMYSLQD NIFN+AV G+FDD QDIVKAVSNDHAFKA+ KIG VNSIN
Sbjct: 181 SPHGKMSAFQRAQMYSLQDDNIFNIAVTGMFDDAQDIVKAVSNDHAFKARHKIGAVNSIN 240

Query: 238 WARVVAQVVYYFKGYFAATRSNDERVSFTVPSGNFGNVCAGHIARMMGLPIEKLVVATNE 297
           WARV AQ+VYYFKGYFAAT SNDE+V+F VPSGNFGN+CAGHIAR MGLP+ KL++ATNE
Sbjct: 241 WARVAAQIVYYFKGYFAATTSNDEQVAFCVPSGNFGNICAGHIARQMGLPVAKLILATNE 300

Query: 298 NDVLDEFFRTGAYRVRSAQDTYHTSSPSMDISKASNFERFVFDLLGRDPARVVQLFRDVE 357
           NDVLDEFFR+G YR R A +T+ TSSPSMDISKASNFERFVFDL+GRDP++V  L+ +V+
Sbjct: 301 NDVLDEFFRSGVYRPRKAAETHVTSSPSMDISKASNFERFVFDLVGRDPSKVAALWAEVD 360

Query: 358 QKGGFDLAASGDFARVAEFGFVSGRSTHADRIATIRDVFERYRTMIDTHTADGLKVAREH 417
               FDL+ + +FAR+  FGFVSG S+HADR+ATIR V+ERY  MIDTHTADG+KVA E 
Sbjct: 361 AGRAFDLSGTDEFARIGAFGFVSGASSHADRLATIRKVYERYGVMIDTHTADGVKVAWER 420

Query: 418 ---LRPGVPMVVLETAQPIKFGESIREALGQEPSRPAAFDGLEALPQRFEVVDANAQQVK 474
              +  GVP++VLETA P+KF E+I EALG+EP RPA  +G+E LPQR EV+  +A  +K
Sbjct: 421 AADVPAGVPVLVLETALPVKFAETIVEALGREPERPADLEGIEKLPQRVEVMAPDADAIK 480

Query: 475 DFIAAHT 481
            FIA  T
Sbjct: 481 RFIAQRT 487


Lambda     K      H
   0.320    0.135    0.392 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 715
Number of extensions: 22
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 483
Length of database: 487
Length adjustment: 34
Effective length of query: 449
Effective length of database: 453
Effective search space:   203397
Effective search space used:   203397
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 bits)

Align candidate WP_004304059.1 C665_RS07145 (threonine synthase)
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00260.hmm
# target sequence database:        /tmp/gapView.21352.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00260  [M=340]
Accession:   TIGR00260
Description: thrC: threonine synthase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
    7.8e-74  234.8   0.0      1e-73  234.4   0.0    1.1  1  lcl|NCBI__GCF_000310185.1:WP_004304059.1  C665_RS07145 threonine synthase


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000310185.1:WP_004304059.1  C665_RS07145 threonine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.4   0.0     1e-73     1e-73      38     331 ..     113     449 ..      98     456 .. 0.89

  Alignments for each domain:
  == domain 1  score: 234.4 bits;  conditional E-value: 1e-73
                                 TIGR00260  38 enlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtgaaaaealagkanvkvvvLy 104
                                                +l ++el+ gPtlaFKD+++q +++l++++l +  e   +l+AtsGdtg+aa +a++gk++v+v++L 
  lcl|NCBI__GCF_000310185.1:WP_004304059.1 113 GRLGLLELSNGPTLAFKDMAMQLLGNLFEYVLAKRGEtiNILGATSGDTGSAAEYAMRGKHGVRVFMLS 181
                                               48999*************************998877735689*************************** PP

                                 TIGR00260 105 Pkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...klklnsvNsinparieaqkty 169
                                               P+gk+s     ++    + n+  +a++G FDdaqd+vk++ +d+     +k+++vNsin+ar++aq++y
  lcl|NCBI__GCF_000310185.1:WP_004304059.1 182 PHGKMSAFqRAQMYSLQDDNIFNIAVTGMFDDAQDIVKAVSNDHAfkaRHKIGAVNSINWARVAAQIVY 250
                                               ********99*******************************96666779******************88 PP

                                 TIGR00260 170 afeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaegaadivrrflksgdlepke 238
                                               +f    +    + ++v++ vpsgnfg+i +G  + +++ lp++kl  a++++ d++++f +sg   p++
  lcl|NCBI__GCF_000310185.1:WP_004304059.1 251 YFKGYFAATTSNDEQVAFCVPSGNFGNICAGHIARQMG-LPVAKLILATNEN-DVLDEFFRSGVYRPRK 317
                                               8875555555899******************8888887.************9.**********666665 PP

                                 TIGR00260 239 dk...eTlstAmdignpsnverale.larrslgnledlke...........................sv 276
                                                     T s++mdi++ sn+er ++ l+ r   ++ +l +                           + 
  lcl|NCBI__GCF_000310185.1:WP_004304059.1 318 AAethVTSSPSMDISKASNFERFVFdLVGRDPSKVAALWAevdagrafdlsgtdefarigafgfvsgAS 386
                                               553456889*************9998**9*99999999889999**********************999 PP

                                 TIGR00260 277 sdeeileaikklaeeegyllephtavavaalkklvekg...vs....atadpaKFeevve.al 331
                                               s ++ l +i+k++e+ g+++++hta +v++  + +++    v      ta p KF+e+++ al
  lcl|NCBI__GCF_000310185.1:WP_004304059.1 387 SHADRLATIRKVYERYGVMIDTHTADGVKVAWERAADVpagVPvlvlETALPVKFAETIVeAL 449
                                               99***************************9888777666541145668999999987766244 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (340 nodes)
Target sequences:                          1  (487 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 8.68
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis